BEGIN:VCALENDAR VERSION:2.0 PRODID:-//Pentabarf//Schedule 0.3//EN CALSCALE:GREGORIAN METHOD:PUBLISH X-WR-CALDESC;VALUE=TEXT:Open Research Tools and Technologies devroom X-WR-CALNAME;VALUE=TEXT:Open Research Tools and Technologies devroom X-WR-TIMEZONE;VALUE=TEXT:Europe/Brussels BEGIN:VEVENT METHOD:PUBLISH UID:13562@FOSDEM22@fosdem.org TZID:Europe-Brussels DTSTART:20220205T100000 DTEND:20220205T100500 SUMMARY:Welcome to the Open Research Tools and Technologies devroom DESCRIPTION:
The Open Research Tools and Technologies devroom managers welcome words announcing the schedule.
CLASS:PUBLIC STATUS:CONFIRMED CATEGORIES:Open Research Tools and Technologies URL:https:/fosdem.org/2022/schedule/2022/schedule/event/open_research_welcome/ LOCATION:D.research ATTENDEE;ROLE=REQ-PARTICIPANT;CUTYPE=INDIVIDUAL;CN="Paul Girard":invalid:nomail ATTENDEE;ROLE=REQ-PARTICIPANT;CUTYPE=INDIVIDUAL;CN="Matthieu Totet":invalid:nomail ATTENDEE;ROLE=REQ-PARTICIPANT;CUTYPE=INDIVIDUAL;CN="Mathieu Jacomy":invalid:nomail ATTENDEE;ROLE=REQ-PARTICIPANT;CUTYPE=INDIVIDUAL;CN="Célya Gruson-Daniel":invalid:nomail ATTENDEE;ROLE=REQ-PARTICIPANT;CUTYPE=INDIVIDUAL;CN="Yo Yehudi":invalid:nomail ATTENDEE;ROLE=REQ-PARTICIPANT;CUTYPE=INDIVIDUAL;CN="Maya Anderson-González":invalid:nomail ATTENDEE;ROLE=REQ-PARTICIPANT;CUTYPE=INDIVIDUAL;CN="Sara Petti":invalid:nomail END:VEVENT BEGIN:VEVENT METHOD:PUBLISH UID:12647@FOSDEM22@fosdem.org TZID:Europe-Brussels DTSTART:20220205T100500 DTEND:20220205T102500 SUMMARY:From pipe dreams and waste to functional accretion: building a capable infrastructure for the Digital Humanities DESCRIPTION:This presentation is about the development and trajectory of Heurist (HeuristNetwork.org), a shared, integrated, extensible data infrastructure (model, build, manage, analyse, visualise, share, publish via integrated CMS) for Humanities research capable of handling the needs of many heterogeneous projects on a single standalone service*, with optional integration across multiple servers by a coordinating index (itself based on Heurist).
Humanities data are interesting (both technically and to the public). They are rich in text, images, objects, people and events, heterogeneous, eminently linkable and sparse-matrix. Personal computers, the internet and other accessible technologies have spawned an exploding field (or fad?) known as Digital Humanities (DH), and opened exciting new horizons for research and public engagement.
However, this technological turn has created many problems for a poorly funded research culture with 1-3 year grant funding cycles - choice of appropriate technology, finding and retaining technical staff, initial and ongoing costs, sustainability ... The outcome is often least-effort and inadequate technology (eg. spreadsheets) or ad hoc development, incomplete functionality, maintenance nightmares, data silos and rapid end-of-funding decay; only rich or statutory organisations can maintain a multi-component system for long. Heurist aims to overcome these problems by mutualised Open Source development, schemas stored as editable data rather than fixed structures, demand-driven priority development, and free centralised services and maintenance.
In this presentation I will outline the evolution of our development process, from haphazard experimentation and many costly unused features (2005 - 2009) to a coherent, stable but evolving structure and Extreme Programming (aka living dangerously!), driven by immediate user requirements and incremental daily interface refinement. I will outline some of the fundamental principles we use to maintain backwards compatibility, stability, rapid development and low cost of maintenance for such a complex beast and for so many projects, on a self-funding staff of just 3 FTE. I also hope to attract some technical collaborators, as most of our users are (by design) non-technical.
CLASS:PUBLIC STATUS:CONFIRMED CATEGORIES:Open Research Tools and Technologies URL:https:/fosdem.org/2022/schedule/2022/schedule/event/open_research_heurist/ LOCATION:D.research ATTENDEE;ROLE=REQ-PARTICIPANT;CUTYPE=INDIVIDUAL;CN="Ian Johnson":invalid:nomail END:VEVENT BEGIN:VEVENT METHOD:PUBLISH UID:12529@FOSDEM22@fosdem.org TZID:Europe-Brussels DTSTART:20220205T102500 DTEND:20220205T104000 SUMMARY:Code Liberation and Software Sustainability DESCRIPTION:Developed from 1995 onward, Prospero is a framework for longitudinal analysis of text corpora. Based on dictionaries and semi-automatic classification, it mainly allows its user to combine approaches of statistical computation, co-occurrence network and search for nested patterns. Inspired by pragmatic sociology, it focuses on the multiple forms of expression and argumentation used by actors, on language regimes and on the identification of transformations occurring in the research case. Initially distributed commercially, then from 2011, by the Doxa association, as shareware under a non-profit and ethical charter, it is now hosted by the Corpora association and developed under the aGPLV3 CECILL variant Affero compliant license.
In this presentation, we will discuss more specifically the question of the permanence of a research-targeted software approach, through its evolution over almost 30 years. During this period, evolving expectations and technical developments have led to a client/server step (which remained in the prototype stage) and now to the transition to SaaS. Based on this experience, we will also discuss the conditions we consider relevant for the durability of the software in a new interconnected phase. The broadening of its audience of users and developers calls for ever greater interoperability, on the technical level, but with an approach that combines non-profit and academic models (with limited resources) and business uses.
Josquin DebazWith a PhD in history of science, he has worked more than 10 years on contemporary controversies in health, environment and energy at GSPR (Pragmatic and Reflexive Sociology Group, EHESS). He is now developer at Finsit. With F. Chateauraynaud, he published Aux bords de l'irréversible. Sociologie pragmatique des transformations (Paris, Pétra, 2017).
Waldir Lisboa RochaWith a degree in Environmental Engineering, he co-founded Luminae, an energy efficiency company, where he served as Chief Operating Officer between 2008 and 2012, before deciding to make a turn in his career and dedicate himself to the Social Sciences. He holds a Master's degree in Sociology from the École des Hautes Études en Sciences Sociales - EHESS, and is currently working on his PhD at the same institution, in which he is focusing on the relations between media, inquiry and democracy. In parallel to his academic research, he has been dedicated to the conception and structuring of Prefigura, an experimental institution, and of Enumera, an operating ecosystem.
CLASS:PUBLIC STATUS:CONFIRMED CATEGORIES:Open Research Tools and Technologies URL:https:/fosdem.org/2022/schedule/2022/schedule/event/open_research_prospero/ LOCATION:D.research ATTENDEE;ROLE=REQ-PARTICIPANT;CUTYPE=INDIVIDUAL;CN="Josquin Debaz":invalid:nomail ATTENDEE;ROLE=REQ-PARTICIPANT;CUTYPE=INDIVIDUAL;CN="Waldir Lisboa Rocha":invalid:nomail END:VEVENT BEGIN:VEVENT METHOD:PUBLISH UID:12546@FOSDEM22@fosdem.org TZID:Europe-Brussels DTSTART:20220205T104000 DTEND:20220205T110000 SUMMARY:Free Software Development as Observant Participation DESCRIPTION:I am a social scientist who mostly teaches and conducts qualitative research, but I am also a programmer. Over the years, I have contributed to a variety of free and open source software projects, and since 2019, I have developed and maintained textnets
, a Python package for text analysis that represents collections of texts as networks of documents and words, providing novel possibilities for the visualization and analysis of texts. In my field, such software development efforts are not usually rewarded, but I have been very fortunate. My academic superiors have been supportive of my endeavors, and a publication in the Journal of Open Source Software also helped me get official recognition for this work in the standard currency of my field.
While I developed textnets
to scratch my own itch, I seek to make the package widely available by providing extensive documentation and making it easily installable across multiple platforms. This part of my software development work -- learning the intricacies of version control, package managers, continuous integration testing, and dependency management -- puts me in a position to learn not just about the technical side of coding, but about the social side of the choices developers make. At least in the Python world, the way you learn about what dependencies to use, if any, and how many, is informed by norms more than by technical considerations, and the same is true for much else. By engaging in software development work, I engage in a version of the research method of participant observation -- learning by taking part -- that sociologists have called observant participation -- becoming part of what you want to learn about. In my case, I want to learn not just about software development and its culture and norms, but the wider world of free software, hacker culture, artistic practice based on FOSS tools, and more.
In my talk, I provide some background to the development of textnets
, give a brief demonstration of the package's features, and finally reflect on my experiences engaging in observant participation as well as some of the insights I have gained and still hope to gain.
Discussion panel of three testimonies from academics developing software.
CLASS:PUBLIC STATUS:CONFIRMED CATEGORIES:Open Research Tools and Technologies URL:https:/fosdem.org/2022/schedule/2022/schedule/event/open_research_testimony/ LOCATION:D.research ATTENDEE;ROLE=REQ-PARTICIPANT;CUTYPE=INDIVIDUAL;CN="Paul Girard":invalid:nomail ATTENDEE;ROLE=REQ-PARTICIPANT;CUTYPE=INDIVIDUAL;CN="Ian Johnson":invalid:nomail ATTENDEE;ROLE=REQ-PARTICIPANT;CUTYPE=INDIVIDUAL;CN="Josquin Debaz":invalid:nomail ATTENDEE;ROLE=REQ-PARTICIPANT;CUTYPE=INDIVIDUAL;CN="John Boy":invalid:nomail ATTENDEE;ROLE=REQ-PARTICIPANT;CUTYPE=INDIVIDUAL;CN="Waldir Lisboa Rocha":invalid:nomail END:VEVENT BEGIN:VEVENT METHOD:PUBLISH UID:12535@FOSDEM22@fosdem.org TZID:Europe-Brussels DTSTART:20220205T112000 DTEND:20220205T114000 SUMMARY:Writing with data visualization DESCRIPTION:The writing of web publications mixing data visualization and textual prose opens novel opportunities for connecting evidence, arguments and narrative in social sciences communities. Such a practice poses a variety of challenges in terms of website design and development ; but also and maybe more importantly, it asks for experimenting specific workflows for coordinating a variety of expertises ranging from social sciences disciplines (history, sociology, etc.) to data science, information design and web-related skills. It also reconfigures, for the research processes themselves, the relationships between activities of (data-related) enquiry and (communication-oriented) writing, creating a renewed space for discovery, invention and verification for the data sustaining a given argument or narrative.
Relying on recent experiments in making collective digital publications grounded in sociology of technology (https://medialab.github.io/carnet-algopresse/#/publication/en) and history of economy (https://medialab.github.io/portic-storymaps-2021/), this talk accounts for the diverse challenges arising from such activities of “data visualization-driven writing”, and some strategies we used to cope with them. It describes and compares the technical and methodological workflows we developed in order to simultaneously develop text, datasets and visualizations, taking into account a variety of aims, data materials, and distribution of skills. Doing so, it advocates for an extended understanding of the notion of “academic writing”, encompassing the practices of writing software, data and diagrams. Such an extended understanding, we argue, is necessary to design and develop writing workflows allowing to foster a multimodal and scientifically productive dialogue between these heterogeneous practices, taking full advantage of the web publication format as a research situation.
CLASS:PUBLIC STATUS:CONFIRMED CATEGORIES:Open Research Tools and Technologies URL:https:/fosdem.org/2022/schedule/2022/schedule/event/open_research_writing_data_visualization/ LOCATION:D.research ATTENDEE;ROLE=REQ-PARTICIPANT;CUTYPE=INDIVIDUAL;CN="Robin De Mourat":invalid:nomail END:VEVENT BEGIN:VEVENT METHOD:PUBLISH UID:12376@FOSDEM22@fosdem.org TZID:Europe-Brussels DTSTART:20220205T114000 DTEND:20220205T120000 SUMMARY:Livemark: data presentation framework DESCRIPTION:This talk will show a new Python tool called Livemark, which is designed for data journalism software education, and documentation writing. Using Livemark, you can collect and present data with interactive tables, charts, and other elements without leaving a text editor. You can also write documentation with live script execution similar to a lightweight version of a Jupiter Notebook. This talk will demo Livemark and will be well-suited for a technical and non-technical audience that is interested in learning about data storytelling.
CLASS:PUBLIC STATUS:CONFIRMED CATEGORIES:Open Research Tools and Technologies URL:https:/fosdem.org/2022/schedule/2022/schedule/event/open_research_livemark/ LOCATION:D.research ATTENDEE;ROLE=REQ-PARTICIPANT;CUTYPE=INDIVIDUAL;CN="Evgeny Karev":invalid:nomail END:VEVENT BEGIN:VEVENT METHOD:PUBLISH UID:12374@FOSDEM22@fosdem.org TZID:Europe-Brussels DTSTART:20220205T120000 DTEND:20220205T121500 SUMMARY:MetaindeX and user requirements for a generic catalog application DESCRIPTION:We will try to define in this presentation basic user needs for a generic working environment on historical data, discuss then some key technologies and architecture orientations for online open-source application MetaindeX, which intends to fulfill those user requirements. At last, we will illustrate its usage with a real corpus of few thousands French archives from "Archives Nationales", from 16th and 17th century.
CLASS:PUBLIC STATUS:CONFIRMED CATEGORIES:Open Research Tools and Technologies URL:https:/fosdem.org/2022/schedule/2022/schedule/event/open_research_metaindex/ LOCATION:D.research ATTENDEE;ROLE=REQ-PARTICIPANT;CUTYPE=INDIVIDUAL;CN="Laurent MILLET-LACOMBE":invalid:nomail END:VEVENT BEGIN:VEVENT METHOD:PUBLISH UID:13031@FOSDEM22@fosdem.org TZID:Europe-Brussels DTSTART:20220205T121500 DTEND:20220205T123500 SUMMARY:Visual inquiries panel DESCRIPTION:Panel discussion between speakers of the visual inquiries session.
CLASS:PUBLIC STATUS:CONFIRMED CATEGORIES:Open Research Tools and Technologies URL:https:/fosdem.org/2022/schedule/2022/schedule/event/open_research_visual_inquiries/ LOCATION:D.research ATTENDEE;ROLE=REQ-PARTICIPANT;CUTYPE=INDIVIDUAL;CN="Robin De Mourat":invalid:nomail ATTENDEE;ROLE=REQ-PARTICIPANT;CUTYPE=INDIVIDUAL;CN="Célya Gruson-Daniel":invalid:nomail ATTENDEE;ROLE=REQ-PARTICIPANT;CUTYPE=INDIVIDUAL;CN="Maya Anderson-González":invalid:nomail ATTENDEE;ROLE=REQ-PARTICIPANT;CUTYPE=INDIVIDUAL;CN="Laurent MILLET-LACOMBE":invalid:nomail ATTENDEE;ROLE=REQ-PARTICIPANT;CUTYPE=INDIVIDUAL;CN="Evgeny Karev":invalid:nomail END:VEVENT BEGIN:VEVENT METHOD:PUBLISH UID:12672@FOSDEM22@fosdem.org TZID:Europe-Brussels DTSTART:20220205T123500 DTEND:20220205T125000 SUMMARY:On the dissemination/evaluation loop for Research Software DESCRIPTION:This talk explores the interconnections that links Research Software (RS) dissemination and evaluation issues, in the Open Science context, following the guidelines of the CDUR RS assessment protocol.
CLASS:PUBLIC STATUS:CONFIRMED CATEGORIES:Open Research Tools and Technologies URL:https:/fosdem.org/2022/schedule/2022/schedule/event/open_research_cdur/ LOCATION:D.research ATTENDEE;ROLE=REQ-PARTICIPANT;CUTYPE=INDIVIDUAL;CN="Teresa Gomez-Diaz":invalid:nomail END:VEVENT BEGIN:VEVENT METHOD:PUBLISH UID:12749@FOSDEM22@fosdem.org TZID:Europe-Brussels DTSTART:20220205T125000 DTEND:20220205T130500 SUMMARY:What is special about open source research software and why does it matters? DESCRIPTION:French citizens have a right to request source code developed by their administration. This includes source code developed by public research labs. But the research sector has a distinct place in the "public code" landscape. It produces open source gems like scikit-learn, and many researchers contribute to Free Software, but some source code is never published because public labs are requested to use them as assets for new startups. This talk will explore this distinct place, the work that has been done in France to promote the publication of research source code and the challenges ahead.
CLASS:PUBLIC STATUS:CONFIRMED CATEGORIES:Open Research Tools and Technologies URL:https:/fosdem.org/2022/schedule/2022/schedule/event/open_research_french_ecosystem/ LOCATION:D.research ATTENDEE;ROLE=REQ-PARTICIPANT;CUTYPE=INDIVIDUAL;CN="Bastien":invalid:nomail END:VEVENT BEGIN:VEVENT METHOD:PUBLISH UID:13042@FOSDEM22@fosdem.org TZID:Europe-Brussels DTSTART:20220205T130500 DTEND:20220205T132500 SUMMARY:Policies panel DESCRIPTION:Discussion between the Policies panel speakers.
CLASS:PUBLIC STATUS:CONFIRMED CATEGORIES:Open Research Tools and Technologies URL:https:/fosdem.org/2022/schedule/2022/schedule/event/open_research_policies/ LOCATION:D.research ATTENDEE;ROLE=REQ-PARTICIPANT;CUTYPE=INDIVIDUAL;CN="Bastien":invalid:nomail ATTENDEE;ROLE=REQ-PARTICIPANT;CUTYPE=INDIVIDUAL;CN="Mathieu Jacomy":invalid:nomail ATTENDEE;ROLE=REQ-PARTICIPANT;CUTYPE=INDIVIDUAL;CN="Teresa Gomez-Diaz":invalid:nomail END:VEVENT BEGIN:VEVENT METHOD:PUBLISH UID:12445@FOSDEM22@fosdem.org TZID:Europe-Brussels DTSTART:20220205T132500 DTEND:20220205T134500 SUMMARY:Ersilia, a hub of AI/ML models for infectious disease research DESCRIPTION:Low and Middle Income Countries (LMIC) produce less than 10% of the world's scientific output, largely relying on solutions devised in the Global North, which are often unable to meet the real needs of their population. Data science and machine learning offer a unique opportunity to empower scientists in LMIC by providing cost-effective tools ideal for underfunded settings, but there is a gap in accessibility, infrastructure and skills that must be bridged before these tools can be effectively implemented.We are developing the Ersilia Model Hub, a FLOSS platform where scientists can browse through a catalogue of AI/ML models and run them without the need to write a single line of code. The platform features both models published in the literature and models developed by us on-demand or in collaboration with researchers in LMIC. The pilot tool focuses on models for drug discovery in infectious and neglected tropical diseases, but we plan to expand to other global health.
CLASS:PUBLIC STATUS:CONFIRMED CATEGORIES:Open Research Tools and Technologies URL:https:/fosdem.org/2022/schedule/2022/schedule/event/open_research_ersilia/ LOCATION:D.research ATTENDEE;ROLE=REQ-PARTICIPANT;CUTYPE=INDIVIDUAL;CN="Gemma Turon":invalid:nomail END:VEVENT BEGIN:VEVENT METHOD:PUBLISH UID:12598@FOSDEM22@fosdem.org TZID:Europe-Brussels DTSTART:20220205T134500 DTEND:20220205T140500 SUMMARY:Improve diagnostics of typhoid through Open Science: An Artificial Intelligence-based technique DESCRIPTION:Typhoid fever is one of the severe infectious human diseases in Africa. Out of an estimated 11–21 million cases of typhoid fever and 200,000 deaths occur worldwide each year. Other elements contribute to this situation and particularly in rural areas where patients to doctors ratio is very low, lack of medical facilities and costly tests. There are a number of tests available presently, from molecular to immunological and biochemical to microbiological. However, Users are unsatisfied due to delays in getting test results and Imprecise diagnosis. Misdiagnosis is usually experienced since most health care facilities use only Widal test without confirmation of results with a second test method. In addition, the diagnosis of Typhoid involves several levels of uncertainties. Patients cannot tell exactly how they feel, doctors and nurses cannot tell exactly what they observe. There is therefore, an urgent need to develop a rapid, highly sensitive and cheap diagnostic tool for diagnosis of typhoid fever.
CLASS:PUBLIC STATUS:CONFIRMED CATEGORIES:Open Research Tools and Technologies URL:https:/fosdem.org/2022/schedule/2022/schedule/event/open_research_diagnostics_typhoid/ LOCATION:D.research ATTENDEE;ROLE=REQ-PARTICIPANT;CUTYPE=INDIVIDUAL;CN="Elisee JAFSIA":invalid:nomail END:VEVENT BEGIN:VEVENT METHOD:PUBLISH UID:13043@FOSDEM22@fosdem.org TZID:Europe-Brussels DTSTART:20220205T140500 DTEND:20220205T142000 SUMMARY:Artificial Intelligence Panel DESCRIPTION:Discussion between the Artificial Intelligence panel's speakers.
CLASS:PUBLIC STATUS:CONFIRMED CATEGORIES:Open Research Tools and Technologies URL:https:/fosdem.org/2022/schedule/2022/schedule/event/open_research_artificial_intelligence/ LOCATION:D.research ATTENDEE;ROLE=REQ-PARTICIPANT;CUTYPE=INDIVIDUAL;CN="Yo Yehudi":invalid:nomail ATTENDEE;ROLE=REQ-PARTICIPANT;CUTYPE=INDIVIDUAL;CN="Elisee JAFSIA":invalid:nomail ATTENDEE;ROLE=REQ-PARTICIPANT;CUTYPE=INDIVIDUAL;CN="Gemma Turon":invalid:nomail END:VEVENT BEGIN:VEVENT METHOD:PUBLISH UID:12783@FOSDEM22@fosdem.org TZID:Europe-Brussels DTSTART:20220205T142000 DTEND:20220205T144000 SUMMARY:GitBuilding: Open source documentation for open source hardware DESCRIPTION:GitBuilding is an Open source program for writing hardware documentation. GitBuilding uses your tags and meta-data to automatically generate and insert bills of materials into your documentation. It correctly links different steps to one another (even when you have multiple variants), allowing you to write instructions once and reuse them for multiple projects. It also shows previews of 3D files and lets you easily include links to generated zips and other files in the correct places. You can output the entire documentation in pure Markdown, HTML, or PDF.
CLASS:PUBLIC STATUS:CONFIRMED CATEGORIES:Open Research Tools and Technologies URL:https:/fosdem.org/2022/schedule/2022/schedule/event/open_research_gitbuilding/ LOCATION:D.research ATTENDEE;ROLE=REQ-PARTICIPANT;CUTYPE=INDIVIDUAL;CN="Julian Stirling":invalid:nomail END:VEVENT BEGIN:VEVENT METHOD:PUBLISH UID:12462@FOSDEM22@fosdem.org TZID:Europe-Brussels DTSTART:20220205T144000 DTEND:20220205T145500 SUMMARY:BeeHive: a flexible open hardware platform for behavioural experiments DESCRIPTION:Digital and technical literacies are an ubiquitous requirement in modern research teams. Despite being fundamental, they are rarely part of the curriculum in universities, thus undergrad and early career researchers often struggle to code data analysis pipelines and to automate data collection from experimental setups. Neurosciences, in particular, relies a lot on these skills, with behavioural experiments planning, design of the testing boxes, data visualisation and analysis. To Successfully complete these tasks, researchers need to acquire a significant level of skill in programming and hardware design.To address these problems, we are developing a flexible open hardware platform to lower the barrier in creating experimental setups: BeeHive. It consists of a main board, which nests an ESP32 microcontroller, and several dedicated “daughter boards”, each designed to perform one function (e.g. one board senses temperature, another controls motors, etc). These boards are connected to one another using a standard system already used by other Open Hardware systems, so that there is no need to reinvent the wheel. We can then focus on developing things that are not available yet. The system runs MicroPython, which is a Python derivative for microcontrollers.This architecture allows users to be in control of everything that the platform is doing while also providing plenty of room for completely new applications. Modular structure helps users to get familiar with electronic components already at entry-level expertise while Python is employed for its strong points such as simplicity and widespread usage. In this presentation we set out to explore the core concept of Beehive, describe existing and possible applications.
CLASS:PUBLIC STATUS:CONFIRMED CATEGORIES:Open Research Tools and Technologies URL:https:/fosdem.org/2022/schedule/2022/schedule/event/open_research_beehive/ LOCATION:D.research ATTENDEE;ROLE=REQ-PARTICIPANT;CUTYPE=INDIVIDUAL;CN="Andre Maia Chagas":invalid:nomail ATTENDEE;ROLE=REQ-PARTICIPANT;CUTYPE=INDIVIDUAL;CN="Ihor Sobianin":invalid:nomail END:VEVENT BEGIN:VEVENT METHOD:PUBLISH UID:13044@FOSDEM22@fosdem.org TZID:Europe-Brussels DTSTART:20220205T145500 DTEND:20220205T151000 SUMMARY:Open Hardware Panel DESCRIPTION:Discussion between the Open Hardware panel's speakers..
CLASS:PUBLIC STATUS:CONFIRMED CATEGORIES:Open Research Tools and Technologies URL:https:/fosdem.org/2022/schedule/2022/schedule/event/open_research_open_hardware/ LOCATION:D.research ATTENDEE;ROLE=REQ-PARTICIPANT;CUTYPE=INDIVIDUAL;CN="Matthieu Totet":invalid:nomail ATTENDEE;ROLE=REQ-PARTICIPANT;CUTYPE=INDIVIDUAL;CN="Andre Maia Chagas":invalid:nomail ATTENDEE;ROLE=REQ-PARTICIPANT;CUTYPE=INDIVIDUAL;CN="Ihor Sobianin":invalid:nomail ATTENDEE;ROLE=REQ-PARTICIPANT;CUTYPE=INDIVIDUAL;CN="Julian Stirling":invalid:nomail END:VEVENT BEGIN:VEVENT METHOD:PUBLISH UID:12540@FOSDEM22@fosdem.org TZID:Europe-Brussels DTSTART:20220205T151000 DTEND:20220205T152000 SUMMARY:Building a consensus meta-data standard for actigraphy and light exposure data DESCRIPTION:In chronobiology and sleep science, researchers often collect data using research-grade activity trackers called actigraphs, which measure movement and determine rest-activity cycles, and light dosimeters, which measure light exposure. At present, there is no meta-data standard for actigraphy and light exposure data that describe aspects of the data collection, such as device manufacturer, sampling rate, or instructions given to the participant. However, meta-data like those are critical for aggregating data and comparing data collected in different samples or across various research sites. Over the past 1+ year, we have been working on developing a consensus meta-data standard for describing actigraphy and light exposure data. The standard is written in JSON-schema, and is extendable to other time-series modalities (such as temperature). The standard is the joint effort of two teams of researchers volunteering their time. In this talk, I will describe the journey from inception to standard, along with the challenges and barriers encountered.
CLASS:PUBLIC STATUS:CONFIRMED CATEGORIES:Open Research Tools and Technologies URL:https:/fosdem.org/2022/schedule/2022/schedule/event/open_research_actigraphy_light_exposure/ LOCATION:D.research ATTENDEE;ROLE=REQ-PARTICIPANT;CUTYPE=INDIVIDUAL;CN="Manuel Spitschan":invalid:nomail END:VEVENT BEGIN:VEVENT METHOD:PUBLISH UID:12506@FOSDEM22@fosdem.org TZID:Europe-Brussels DTSTART:20220205T152000 DTEND:20220205T153000 SUMMARY:BrAPI: a standard API specification for plant breeding data DESCRIPTION:Modern plant breeding research requires a large amount of data to function effectively. Data repositories are improving in their ability to store this data, but there is a growing need for interoperability between disparate data sources and applications. The Breeding Application Programming Interface (BrAPI) project offers a solution to this problem with a standardized RESTful web service API specification. This specification provides a standard data model for the plant breeding domain, plus a well-defined set of methods for interacting with the data. The goal of the project is to promote interoperability, data sharing, and open source code sharing across organizations who produce and consume data in this domain. The BrAPI project is a community built project and that community is well established and continuously growing. The standard is built based on concrete use cases to solve real interoperability challenges faced by the community. Beyond the core standard, the community has built a variety of open source tools and resources to help build and test implementations of the specification. The community is also constantly producing new BrAPI compliant applications, analysis tools, and visualizations that will work with any BrAPI data source.
CLASS:PUBLIC STATUS:CONFIRMED CATEGORIES:Open Research Tools and Technologies URL:https:/fosdem.org/2022/schedule/2022/schedule/event/open_research_brapi/ LOCATION:D.research ATTENDEE;ROLE=REQ-PARTICIPANT;CUTYPE=INDIVIDUAL;CN="Peter Selby":invalid:nomail END:VEVENT BEGIN:VEVENT METHOD:PUBLISH UID:13045@FOSDEM22@fosdem.org TZID:Europe-Brussels DTSTART:20220205T153000 DTEND:20220205T155000 SUMMARY:Standards panel DESCRIPTION:Discussion between Standards panel's speakers.
CLASS:PUBLIC STATUS:CONFIRMED CATEGORIES:Open Research Tools and Technologies URL:https:/fosdem.org/2022/schedule/2022/schedule/event/open_research_standards_panel/ LOCATION:D.research ATTENDEE;ROLE=REQ-PARTICIPANT;CUTYPE=INDIVIDUAL;CN="Mathieu Jacomy":invalid:nomail ATTENDEE;ROLE=REQ-PARTICIPANT;CUTYPE=INDIVIDUAL;CN="Peter Selby":invalid:nomail ATTENDEE;ROLE=REQ-PARTICIPANT;CUTYPE=INDIVIDUAL;CN="Manuel Spitschan":invalid:nomail END:VEVENT BEGIN:VEVENT METHOD:PUBLISH UID:12362@FOSDEM22@fosdem.org TZID:Europe-Brussels DTSTART:20220205T155000 DTEND:20220205T161000 SUMMARY:Ontology Development Kit DESCRIPTION:In biomedical sciences, ontologies are used to annotate and organize data stored in knowledge databases and facilitate their exploitation. Following the pioneering work of the Gene Ontology at the turn of the century, the Open Biomedical and Biological Ontologies (OBO) Foundry was created to coordinate the development of a family of interoperable ontologies sharing a core set of principles. The Foundry now includes more than 150 ontologies.The Ontology Development Kit (ODK) [1] was developed to facilitate the implementation of standardized ontology development practices across the Foundry. It takes the form of a Docker image that provides ontology editors with all the command-line tools they need to manage, edit, build, and test their ontologies, as well as standardized and carefully crafted Makefile rules to pilot all steps of the ontology life cycle. In recent years, many ontologies such as the Uberon multi-species anatomy ontology, the Cell Ontology (CL), or the Unified Phenotype Ontology (uPheno) have been converted to use the ODK. By moving most of the management, building, and testing logic from the individual ontologies to the ODK, the kit aims to make the life of ontology editors easier, by allowing them to focus solely on actual ontology editing, all the while contributing to the standardisation of the various ontologies.
CLASS:PUBLIC STATUS:CONFIRMED CATEGORIES:Open Research Tools and Technologies URL:https:/fosdem.org/2022/schedule/2022/schedule/event/open_research_ontology_development_kit/ LOCATION:D.research ATTENDEE;ROLE=REQ-PARTICIPANT;CUTYPE=INDIVIDUAL;CN="Damien Goutte-Gattat":invalid:nomail END:VEVENT BEGIN:VEVENT METHOD:PUBLISH UID:12507@FOSDEM22@fosdem.org TZID:Europe-Brussels DTSTART:20220205T161000 DTEND:20220205T163000 SUMMARY:Sustainable community building with the Wikibase Stakeholder Group DESCRIPTION:The Wikibase Stakeholder Group is a new initiative testing alternative approaches to governance, decision-making and community-building for open source digital knowledge management. It aims to facilitate collaboration across various institutional and individual partners in order to ensure the continued development and long-term sustainability of Wikibase, a suite of tools for data management within a linked open data environment. Wikibase is currently developed and maintained by Wikimedia Germany, a chapter of the non-profit Wikimedia Foundation. Wikibase is vital infrastructure for the public linked data project Wikidata, but since its open release in 2015 it has been increasingly taken up in research, cultural and institutional contexts due to its flexible, open and collaborative architecture. Rhizome have been piloting the use of Wikibase within GLAM contexts since its release, and have co-organized the first set of public meetups and events around the emerging Wikibase community and ecosystem of decentralized Wikibase instances. Following the success in bringing the community together through these events Rhizome and a few early adopters started the Wikibase Stakeholder Group at the end of 2020. In this talk, we will present the activities of the Group to date, lessons learned from our experiences in collective decision-making, funding for collaborative development efforts, and negotiating between individual project requirements towards a common roadmap in line with ongoing efforts of the Wikimedia team.
CLASS:PUBLIC STATUS:CONFIRMED CATEGORIES:Open Research Tools and Technologies URL:https:/fosdem.org/2022/schedule/2022/schedule/event/open_research_wikibase/ LOCATION:D.research ATTENDEE;ROLE=REQ-PARTICIPANT;CUTYPE=INDIVIDUAL;CN="Lozana Rossenova":invalid:nomail ATTENDEE;ROLE=REQ-PARTICIPANT;CUTYPE=INDIVIDUAL;CN="Dragan Espenschied":invalid:nomail END:VEVENT BEGIN:VEVENT METHOD:PUBLISH UID:13039@FOSDEM22@fosdem.org TZID:Europe-Brussels DTSTART:20220205T163000 DTEND:20220205T164500 SUMMARY:Knowledge management communities panel DESCRIPTION:Discussion between speakers of the Knowledge Management Communities panel.
CLASS:PUBLIC STATUS:CONFIRMED CATEGORIES:Open Research Tools and Technologies URL:https:/fosdem.org/2022/schedule/2022/schedule/event/open_research_knowledge_management_panel/ LOCATION:D.research ATTENDEE;ROLE=REQ-PARTICIPANT;CUTYPE=INDIVIDUAL;CN="Paul Girard":invalid:nomail ATTENDEE;ROLE=REQ-PARTICIPANT;CUTYPE=INDIVIDUAL;CN="Damien Goutte-Gattat":invalid:nomail ATTENDEE;ROLE=REQ-PARTICIPANT;CUTYPE=INDIVIDUAL;CN="Lozana Rossenova":invalid:nomail ATTENDEE;ROLE=REQ-PARTICIPANT;CUTYPE=INDIVIDUAL;CN="Dragan Espenschied":invalid:nomail END:VEVENT BEGIN:VEVENT METHOD:PUBLISH UID:13519@FOSDEM22@fosdem.org TZID:Europe-Brussels DTSTART:20220205T164500 DTEND:20220205T170000 SUMMARY:F-UJI : A Tool for the automated assessment and improvement of the FAIRness of Research Data DESCRIPTION:Funders, publishers and scientific organizations have highly endorsed the adoption of FAIR principles (Findable, Accessible, Interoperable, and Reusable) to promote research data reusability and reproducibility.However, FAIR principles are high-level guidelines without explicit requirements for their implementation. Practical solutions such as metrics and associated tools are required to support the assessment of FAIR compliance of research artefacts such as services and datasets. This talk will introduce an open-source tool named F-UJI which was mainly developed to support trustworthy data repositories committed to FAIR data provision to programmatically measure datasets for their level of FAIRness over time. The talk will provide an overview the development and application of F-UJI and use cases it has supported so far.
CLASS:PUBLIC STATUS:CONFIRMED CATEGORIES:Open Research Tools and Technologies URL:https:/fosdem.org/2022/schedule/2022/schedule/event/open_research_f_uji/ LOCATION:D.research ATTENDEE;ROLE=REQ-PARTICIPANT;CUTYPE=INDIVIDUAL;CN="Patricia Herterich":invalid:nomail END:VEVENT BEGIN:VEVENT METHOD:PUBLISH UID:12771@FOSDEM22@fosdem.org TZID:Europe-Brussels DTSTART:20220205T170000 DTEND:20220205T172000 SUMMARY:Internal R packages for Open Science in Agrometeorology DESCRIPTION:Argentina's National Institute of Agricultural Technology (INTA) conducts research and development for the agricultural sector. Environmental conditions influence agricultural activity; in particular, climatic conditions have a favorable or detrimental effect on production. Thus, it is essential to monitor and analyze the different agro-meteorological variables to describe these conditions and their impact on agricultural and livestock production. With this approach, INTA has an extensive ground network of conventional and automatic weather stations. In addition, there is an information system (http://siga.inta.gob.ar) with predefined queries and visualization on this data for internal and external use. All the information generated by the institution is openly shared under a CC-BY-NC license.INTA is a decentralized institution and generates research, analysis, and reports at different scales (national to local). The processes to perform these tasks use various software tools and different methodologies. Moreover, these processes are in the computer and the head of the researchers.
Developing internal packages or libraries has great potential to promote reproducible analysis frameworks, improve an organization's code quality, enhance knowledge management (Riederer, 2021), standardize and make processes transparent, and open software and data to society.
The {agromet} package includes a series of functions that can be used regularly for the calculation of agrometeorological indices and statistics. The input meteorological data works under the tidy data philosophy, so the package functions are generic. They can be applied to any tabular dataset regardless of its origin, order, or column names. However, according to INTA's internal requirements, the package also incorporates tools to read data in an INTA format. This package has implemented functions for calculating indexes and variables of agricultural interest, standardizing how these computations are made. It also incorporates mapping functions with scale and reports templates.
The package {siga} downloads and reads data from INTA's Agrometeorological Information and Management System programmatically.
This talk will discuss the decision process to generate a series of internal packages designed to be used by INTA users but with enough generality to be helpful to a broad community. Their development, current use, and this experience encouraged the generation of similar packages for soil data.
CLASS:PUBLIC STATUS:CONFIRMED CATEGORIES:Open Research Tools and Technologies URL:https:/fosdem.org/2022/schedule/2022/schedule/event/open_research_agrometeorology/ LOCATION:D.research ATTENDEE;ROLE=REQ-PARTICIPANT;CUTYPE=INDIVIDUAL;CN="Yanina Bellini Saibene":invalid:nomail END:VEVENT BEGIN:VEVENT METHOD:PUBLISH UID:12758@FOSDEM22@fosdem.org TZID:Europe-Brussels DTSTART:20220205T172000 DTEND:20220205T174000 SUMMARY:Unveiling Hidden Physics at the LHC using Open Data DESCRIPTION:The experiments at the Large Hadron Collider (LHC) at CERN have been running for more than a decade. The data recorded by the detectors such as the CMS experiment are analysed by thousands of physicists all over the world. The CMS Collaboration has made openly available more than 2.5 petabytes of data on the CERN Open Data Portal, containing billions of recorded and simulated events.
Open Data are, however, only useful when accompanied by realistic usage examples. The sheer amount of data as well as the fact that the software used to analyse them is often more than ten years old poses several challenges. In this presentation, Clemens will discuss how the CMS Data Preservation and Open Access group tries to overcome these challenges so that potentially everyone could use the data to unveil hidden physics.
CLASS:PUBLIC STATUS:CONFIRMED CATEGORIES:Open Research Tools and Technologies URL:https:/fosdem.org/2022/schedule/2022/schedule/event/open_research_lhc/ LOCATION:D.research ATTENDEE;ROLE=REQ-PARTICIPANT;CUTYPE=INDIVIDUAL;CN="Clemens Lange":invalid:nomail END:VEVENT BEGIN:VEVENT METHOD:PUBLISH UID:13040@FOSDEM22@fosdem.org TZID:Europe-Brussels DTSTART:20220205T174000 DTEND:20220205T180000 SUMMARY:Open Data Panel DESCRIPTION:Discussion between the Open data Panel speakers.
CLASS:PUBLIC STATUS:CONFIRMED CATEGORIES:Open Research Tools and Technologies URL:https:/fosdem.org/2022/schedule/2022/schedule/event/open_research_open_data_panel/ LOCATION:D.research ATTENDEE;ROLE=REQ-PARTICIPANT;CUTYPE=INDIVIDUAL;CN="Sara Petti":invalid:nomail ATTENDEE;ROLE=REQ-PARTICIPANT;CUTYPE=INDIVIDUAL;CN="Yanina Bellini Saibene":invalid:nomail ATTENDEE;ROLE=REQ-PARTICIPANT;CUTYPE=INDIVIDUAL;CN="Clemens Lange":invalid:nomail ATTENDEE;ROLE=REQ-PARTICIPANT;CUTYPE=INDIVIDUAL;CN="Patricia Herterich":invalid:nomail END:VEVENT END:VCALENDAR